One: Why you doing it that way, you know you can have Euae, and simply have the real amiga OS3.9 installed for your A2000??
Two: How are you doing your formatting procedure?? Through the installer?
Three: I had a similar problem with AROS on x86 hardware. So, I let it boot up from the cd, any chance you can do this, just to get the formatting done?(OS3.9)
Four: If your doing it via Amiga forever, forget it. You will need to format it with windows or linux as the base OS. Then install winUAE via AF or the like, amithlon and amikit can also be done.
Five: It seems you need to manually make your computer recognise that you have a HD installed perhaps??
Six: On the amiga forever website, there is a guide on how to install winUAE as your main bootable OS, and it wont show windows or linux at all.
But, I believe you would still require one of those other os's to be installed as a base platform for Winuae to work.
OK
Well, I may have indirectly helped you, who knows, but definately check out AF website, cloanto has a guide there for things like this by memory.